Aspartame is in part excreted by a genetically modified bacteria, with an added amino acid.
http://www.independent.co.uk/news/worlds-top-sweetener-is-made-with-gm-bacteria-1101176.html
It is not technically GMO because there is no modified DNA in the final product. Still, it is not naturally produced. It is, however, still able to be classed under the label "natural flavoring".

Aspartame has also been found to be carcinogenic by the European Ramazzini Foundation
http://www.laleva.org/eng/2006/05/european_ramazzini_foundation_stands_behind_aspartame_study_results_announces_ongoing_research_on_artificial_sweeteners.html
The FDA, predictably, does not concur.